I note I do not think Woese should win a Nobel for discovering the archaea. That was a groundbreaking finding but it does not fit well with the Nobel Prize categories. I think he should win it for the concept of molecular classification of microorganisms and applying this in general to the microbial world around us. This concept (expanded by Norm Pace and colleagues to uncultured microbes) revolutionized our approach to studying single microbes in the environment, to studying single microbes infecting people and to studying communities of microbes in and on people. And thus Woese and Pace in my opinion deserve the Nobel Prize for Medicine. I will be expanding on this in a future post ...

“We find little constructive dialogue can be had on blogs and other listservs where logic, balance and common courtesy are not practiced and observed,” Glenn S. Ruskin, the group’s director of public affairs, said in an e-mail message. “As a matter of practice, ACS finds that direct engagement via telephone or face-to-face with individuals expressing concern over pricing or other related matters is the most productive means to finding common ground and resolution."

Then he attempted to clarify some details of the quote in that he claimed that the following got left off the end of the quote "Therefore, we will not be offering any response to this blog posting or the conversation that has ensued." but when doing this he got a bit personal and nasty:

The individual responsible for the above cited blog certainly has the right to her opinion, but that does not excuse rude behavior or her use of profanity and vulgarity in addressing ACS or its employees. While not evident in the most recent postings, I won’t repeat what she has posted in the past. But I think you would agree that vulgarity and profanity postings do not lend themselves to meaningful, productive and civil discourse, thus our decision not to engage any further with her on this topic

And the discussion continued on various blogs like Chembark. The most disturbing part to me of the whole thing is that it is hard to find anything particularly extremely vulgar in writings by Jenica Rogers (I note - I only googled around for a minute or so so I may have missed things but Walk Walt at Random has more detail on this and also did not find any serious vulgarity). Generally I find the response of ACS to be extremely distasteful. They don't like what she wrote. So they go after her character. Brilliant.

You see, an opera singer work a "head-mounted, face-clinging device" which contained within in some algae in water. And then the algae was fed by the opera singer's breath. This is part of something called the "Algae Opera". The most amazing part of this is described in the io9 article

"Because the algae's growth is dependant on the amount of CO2 it receives, the singer controlled her pitch and volume to alter various characteristics of the algae, including taste (what they called "sonic enhancement"). Depending on the way she sang, the different pitches and frequencies could make the food taste either bitter or sweet"

And then at the end of the performances the audience was invited to sample some of the algae. Yum. Certainly a bit weird. But kudos on the creativity index.

Wednesday, September 26, 2012

A new paper is getting some press on a link between type II diabetes and the microbiome. The paper is here. The abstract of the paper reads:

Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.

Seems pretty reasonable. All they say there is that they found associations between bacteria and diabetes. That is interesting but they do not seem to present any evidence about a causal connection. Perhaps people who get type II diabetes end up then having their microbiome shift. Perhaps a shift in the microbiome causes type II diabetes. Or perhaps something else (e.g., excessive inflammation) causes both type II diabetes and microbiome shifts. Who knows.

"I think our study provides many targets for disease prevention and treatment through gut microbiotia in the near future," said study senior author Jun Wang, executive director of the Beijing Genomics Institute in Shenzhen, China.

Fortunately the reporter who wrote this story does a very good job of providing cautious interpretations. See for example:

"There's no way right now that you can say there's a cause-and-effect relationship. It could be that the patients with diabetes were treated with drugs that changed their gut flora. Or maybe they ate differently? This is an interesting hypothesis -- that gut bugs could influence diseases states -- but it's far from proven," said Dr. Stuart Weinerman, associate chief of the division of endocrinology at North Shore University Hospital/Long Island Jewish Medical Center in New Hyde Park, N.Y.

Also see stories like Gut bacteria could cause diabetes from Science Codex. The title alone makes me want to cry. Some quotes as well as discussion in that article also seem, well, not cautious enough.

The research, which was recently published in the scientific journal Nature, also demonstrated that people with type 2 diabetes have a more hostile bacterial environment in their intestines, which can increase resistance to different medicines.

Definitely not buying this "hostile" environment claim. Fortunately as with the US News story, there is some caution presented

"It is important to point out that our discovery demonstrates a correlation. The big question now is whether the changes in gut bacteria can affect the development of type 2 diabetes or whether the changes simply reflect that the person is suffering from type 2 diabetes."

So - the stories seem to actually be doing an OK job with the correlation vs. causation issue I have complained about many times. And though some of the scientists may be pushing a bit of overinterpretation the reporters and even the press releases have some decent cautionary statements.

Friday, September 21, 2012

Woohoo. Just discovered a cool (I think new) thing. Was looking for a link to a new publication of mine. And I searched Google Scholar

That gets my publications but they are sorted by citation number which alas does not pull up new publications. So I went to click on the "Since 2012" button I usually click on

And I noticed something I have not noticed before (and that I think must be pretty new):

Woohoo - a full sort by date option. And so I clicked it and indeed it did work.

This will make Google Scholar much more useful for certain purposes. This - along with other new features such as the Google Scholar "Updates" system is giving me hope that Google will continue to expand the tools/features of Google Scholar.

Phylogenetic trees of present-day species allow inference of the rate of speciation and extinction which led to the present-day diversity. Classically, inference methods assume a constant rate of diversification, or neglect extinction. I will discuss major limitations of this null model and will present a new framework which allows speciation and extinction rates to change through time (environmental-dependent diversification), with the number of species (density-dependent diversification), and with a trait of a species (trait-dependent diversification). For the latter model, particular focus is given to the trait being the age of a species. Issues arising in empirical data analysis, such as incomplete taxon sampling, model selection, and confidence interval estimation, will be discussed. The methods reveal interesting macroevolutionary dynamics for mammals, birds and ants, and can easily be applied to other datasets using the R packages TreePar and TreeSim available on CRAN.

Monday, September 17, 2012

I have been wanting to start a new series here on my blog about examples of great writing in scientific publications. There is a lot out there on great science writing. But that is not what I am writing about here. I mean actual scientific research papers where the writing itself is exceptional. And todays example, which may be a bit unfair, comes from the one and only Vladimir Nabokov. For not only was he a great writer of literature, he was also a lepidopterist. He was for some time the curator of leps at the Harvard Museum of Comparative Zoology.

I note - I first discovered this when I got a work-study job shelving books at a library at Harvard only to discover that that library had on display a collection of Nabokov's butterflies. I got little shelving done when nobody else was around).

Anyway, I had read some of his short stories and book in high school but was not aware of his butterfly obsessions. What amazed me most was they had some of his butterfly research papers on display too and they were simply amazing to read. The writing in them is just awesome.

So thus we get to todays's example of great writing in science papers: Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera). Thankfully, somehow, Hindawi publishers have come into possessing of the rights to the back issues of the journal Psyche where this was published and it is freely available as a PDF. The paper is not perfect mind you - some parts are written more eloquently than others. But there are sparks in there of what I think are wonderful (for a science research papers). Some of my favorite parts are quoted below:

The results proved so unexpected and interesting that it seems worth while to publish the present paper despite its rather superficial and incomplete nature.

In a way the initial blunder was Swinhoe’s who while correctly giving a subfamilial ending to the group which Tutt’s intuition and Chapman’s science had recognized ("tribe" Plebeidi which exactly corresponds to the Plebefine of Sternpffer) as different from other "tribes" (i.e., subfamilies) within the Lyccenidce, failed to live up to the generic diagnoses which he simply copied from Chapman’s notes in Tutt and tried to combine genitalic data he had not verified or did not under- stand with the obsolete "naked v. hairy eyes" system (which at Butler’s hands had resulted in probably the most ludicrous assembly of species ever concocted, see for example Butler 1900, Entom. 33: 124), so that in the case of several Indian forms which Chapman had not diagnosed, Swinhoe placed intra-
generically allied species in different subfamilies and species belonging to different Tuttian "tribes" in the same subfamily. [[ YES - THIS IS ONE SENTENCE]]

The arrangement proposed in the present paper needs to be prefaced by a few words on taxonomic units. The strictly biological meaning forcibly attached by some modern zoologists to the specific concept has crippled the latter by removing the morphological moment to a secondary or still more negligible position, while employing terms, e.g., "potential interbreeding," that might make sense only if an initial morphological approach were presupposed.

I am sure there are other Nabokov papers with other choice sections ... will be looking for those later. If anyone has suggestions for other great writing in science papers, please post comments ..

Saturday, September 15, 2012

So when this press release about microbes and hyenas came out: Microbes help hyenas communicate via scent I wanted to write about it. But I could not figure out what I thought about the story. Still don't know what I think but it is interesting and worth sharing. Also see the original paper:

3. I see no evidence that the type of analysis that they do on protein folds is a robust phylogenetic method. Phylogeny from sequence alignments (which is what we focus on in my lab) have been tested and tweaked for some 50 years. There are 100s to maybe 1000s of papers on methods alone - not to mention the 1000s of papers using alignments for phylogenetics. I am not convinced that the analysis being done here of FFs and FSFs is particularly robust. It seems interesting, certainly. But is it sound? I mean, I could build phylogenetic trees from cell size, from shape, from eye color, and from all sorts of other features. Those would all suck for certain. Protein folds - not sure about them. They almost certainly are prone to convergent evolution and I do not see any attempt in this analysis to deal with that issue.

4. The authors of the current paper do not show any taxa names on their trees - just colors for large groups of taxa (bacteria, archaea, eukaryotes and viruses). It is really not good practice to remove the taxon names. If they were there the first thing I would do is to look at the patterns within the groups they highlight. Do all the major phyla / kingdoms of eukaryotes, for example, come out looking as one would expect based upon other studies. Or are they all over the place? Same for bacteria and archaea. Not including taxa makes it nearly impossible to judge this paper positively. I could not find this information in supplemental data either.

5. They really should have released the data tables they used for the phylogenetic analysis. Don't know why they did not.

6. In Figure 3 with the rooting they have, either viruses are a subgroup of archaea or archaea are not monophyletic. Not a good thing in a paper trying to claim viruses represent a fourth grouping on the tree of life.

Anyway - got to do some other things but just wanted to get some comments out there.

UPDATE 9/19 - some prior stories about the "fourth domain" and ancient viruses - to counter notion in the press release for this paper that their findings "shake up the tree of life". Even if their specific inferences about viral evolution are correct, such inferences / conclusions have been made before.

Wednesday, September 12, 2012

Many years ago I served on a NASA sponsored committee for a series of meetings about the handling of samples collected from Mars. One of the key points of discussion at those meetings was "planetary protection". The involved protecting Earth from possibly strange life forms that in theory could exist on Mars. And it also involved protecting Mars from microbes and other life forms that could come from space ships/landers. I even posted all the materials from these meetings a few weeks ago: Notes and materials from MARS Sample Handling Workshops 2000 ....

It is thus with great distress that I read an LA Times article that reveals that some of the people involved in launching Curiosity decided to ignore some of the planetary protection guidelines and made some hands on modifications that may have contaminated some of the drill bits on Curiosity with microbes from people. See: If the Mars rover finds water, it could be H2 ... uh oh! - latimes.com.

The LA Times reports that some NASA personnel opened a box of drill bits that had been sterilized and - in clean but not sterile conditions - installed one of these drill bits in a drill on Curiosity prior to launch. Apparently they were worried that a rough landing could prevent the bits from being installable in the drill which would make the drill not be of any use. And they appear to have now risked the sterility of the entire operation by doing this. Well crap. That just plain sucks. So much effort by "planetary protection officers" and others. That effort might all go down the drain because of this. I get that some times things seem urgent and that sure - if the drill was useless people would be pretty upset too. But this seems to me to be a serious error in judgement.

In a small way I helped develop the guidelines that were put in place to protect Mars from human induced contamination. And now that seems to have been a wasted effort as the guidelines were ignored. Not good.

Note - for those interested I have posted links below to the documents from my days at the NASA Mars Sample Handling Workshops. Most/all are public domain materials but not all are easy to find so I thought I would post them here. Note – I have done no clean up of scans – will do so at some point. Enjoy

Well, I mean - who wouldn't want to go to Hawaii for a meeting. And a meeting that

"brings together scientists and engineers who are interested in all areas of q-bio."

Plus

"Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio."

So I could go to Hawaii each year. Cool. And

"The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area."

I like synthetic biology and, well, sometimes I like experts, so still good

But then, OMG, then, the confirmed speaker list and the conference organizers.

2013 CONFIRMED SPEAKERS:

Jim Collins, Boston University

Johan Elf, Uppsala University

Michael Elowitz, California Institute of Technology

Timothy Elston, UNC Chapel Hill School of Medicine

James E. Ferrell, Stanford University

Martin Fussenegger, ETH Zurich

Leon Glass, McGill University

Terry Hwa, University of California, San Diego

Roy Kishony, Harvard Medical School

Galit Lahav, Harvard University

Andre Levchenko, Johns Hopkins University

Wendell Lim, University of California, San Francisco

Andy Oates, The Max Planck Institute, Dresden

Bernhard Palsson, University of California, San Diego

Gurol Suel, UT Southwestern Medical Center

Chao Tang, Peking University

John Tyson, Virginia Tech

Craig Venter, The J. Craig Venter Institute

Chris Voigt, Massachusetts Institute of Technology

Ned S. Wingreen, Princeton University

CONFERENCE ORGANIZERS:

Bill Ditto, University of Hawaii

Jeff Hasty, UC San Diego

Bill Hlavacek, University of New Mexico

Alex Hoffmann, UC San Diego

Brian Munsky, New Mexico Consortium

Lev Tsimring, UC San Diego

That is a 25:1 ratio. Pathetic. Embarrassing. The sponsors - UC San Diego's Division of Biological Sciences and BioCircuits Institute, San Diego Center for Systems Biology, the University of Hawaii and the Office of Naval Research - should all be ashamed.For other posts on this topic see

UPDATE - I have now submitted an abstract to the meeting. The abstract I submitted is available here and posted below

The probability of having one out of twenty six participants at a scientific meeting be female

A quantitative analysis of gender bias in quantitative biology meetings

Jonathan A. Eisen

University of California, Davis

(Note - new title suggested by John Hogenesch)

Scientific conferences have key participants which I define to be the speakers and the organizers. Such key participants can be divided into two main classes based on gender: male and female, which I denote here as M and F, respectively (I realize there are other gender classes and I regretfully am not including them here). The number of key participants (which I denote as KP) for conferences varies significantly. For this analysis I focused on meetings with KP = 26. This value was selected for multiple reasons, including (a) that it is the number of letters in the English alphabet (b) that its factors include the number 13 which I like, and (3) because in email announcements for this meeting KP= 26. I sought to answer a relatively simple question - what is the probability that, for a meeting with KP=26, that F = 1. I chose this because this seemed extreme and because F=1 in the email announcements for this meeting. Using the probability mass distribution formula as below:

which becomes

n = NP = number of participants
k = f = the number that are female
p = percentage of f in population being sampled

I have calculated Pr (F=1) for KP = 26. Assuming for the moment that p = 0.5 (i.e., that the population to be sampled is 50:50 male vs female) then Pr (F=1) = 3.8743E-07. This is highly unlikely by chance alone. However the assumption of p = 0.5 is certainly off in some fields. I therefore calculated P (F=1) for different frequencies of F in the population (i.e., what is the expected ratio of females to sample from).

Thus for a meeting with NP = 26, only when the frequency of F is ~0.16 does P (F=1) exceed 0.05. So a question is then, what should we use for p for this meeting? An informal survey (John Hogenesch, posted to Facebook at https://www.facebook.com/jonathaneisen/posts/10151208978630767?comment_id=24634832&offset=0&total_comments=15 ) suggests that in qBio the percentage is about 20%. However that may not be an ideal estimate since this meeting is specifically about synthetic biology, I do not have a any estimate of p for this field. However, examination of key meetings in the field (e.g., see http://syntheticbiology.org/Conferences.html for a list) reveals a percentage of perhaps a bit higher. For example at SB5 the ratio was about 35%. I conclude that it is likely that p > 20% in Synthetic Biology. Given that for p = 0.2 the Pr (F=1) < 0.05 I therefore conclude that the null hypothesis (that having one female out of 26 key participants) can be rejected - and that this meeting has a biased ratio of males: females.

THE FIRST ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 18-21, 2013http://w-qbio.org/

The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio. The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area.

SPONSORED BY:UC San Diego's Division of Biological Sciences and BioCircuits Institute
San Diego Center for Systems Biology
University of Hawaii
Office of Naval Research

HOTEL: A block of rooms have been reserved for registered conference participants available for a negotiated rate of $199 per night at the Hilton Hawaiian Village in Waikiki. The rooms are available on first come first serve basis and will be available soon, so book early!

CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the September 15th deadline. Abstract guidelines and submission information at:http://w-qbio.org/guidelines.pdf

ABSTRACT DEADLINE: September 15, 2012
Accepted abstracts will be announced October 31, 2012.

We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.

UPDATE: In response to participant interest, the submission deadline has been extended to December 2, 2013. This year 15 contributed talks will be selected from the submitted abstracts to be presented with the invited talks during the plenary sessions. Contributed talks will also be selected for parallel breakout sessions which commence in the late afternoon.

THE SECOND ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 17-20, 2014
http://w-qbio.org/

The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. The venue for 2014 is the Hilton Waikoloa Village, which is located on the Kohala Coast of Hawaii’s Big Island. The resort lets you experience breathtaking tropical gardens, abundant wildlife, award-winning dining, world-class shopping, art and culture, and an array of activities. The Island of Hawaii is the youngest and biggest in the Hawaiian chain, providing a vast canvas of environments to discover--home of one of the world’s most active volcanoes (Kilauea), the most massive mountain in the world (Maunaloa), and the largest park in the state (Hawaii Volcanoes National Park).

SPONSORED BY:
UC San Diego BioCircuits Institute and the San Diego Center for Systems Biology
The University of Hawaii at Manoa
UC San Diego Divisions of Biological Sciences and Engineering
The Office of Naval Research

CONFERENCE ORGANIZERS:
Kevin Bennett, University of Hawaii at Manoa
William Ditto, University of Hawaii at Manoa
Hana El-Samad, University of California, San Francisco
Jeff Hasty, University of California, San Diego
Alexander Hoffmann, University of California, San Diego
Galit Lahav, Harvard University
Eva-Maria Schoetz-Collins, University of California, San Diego
Chao Tang, Peking University
Lev Tsimring, University of California, San Diego

HOTEL: A block of rooms has been reserved for registered conference participants at a negotiated rate of $199 per night at the Hilton Waikoloa Village. The rooms will be available soon on a first-come, first-served basis, so book early!

CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the November 5th deadline. Abstract guidelines and submission information at: http://w-qbio.org/abstracts/

ABSTRACT DEADLINE: EXTENDED UNTIL MONDAY, December 2, 2013 (Extended due to large volume of interest!)
Accepted abstracts will be announced by December 6, 2012. You may submit your abstract now and if accepted, still register by the early bird registration deadline of December 20, 2013.
Abstract guidelines and submission information at: http://w-qbio.org/abstracts/

We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.

I just can't keep up. These seem like they might be worth reading. But no time to blog about them. So here are some possible things to look at if you care about obesity and its possible connection to the microbiome.